It is an extension to Diamond's checkerboard score (See references below) to ordinal data and implements a
framework for robust detection of species-level association patterns in metagenomic data.

Usage

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Arguments

x

A numeric vector, data frame, or matrix. The first entity to be processed. Columns are bugs, rows are samples.

y

NULL(default) or a umeric vector, data frame, or matrix with
compatible dimensions to x. Columns are features, rows
are samples.

use

An optional character string givinga method for computing covariances
in the presence of missing values. This must be (an abbreviaion of)
on of the strings "everything", "all.obs",
"complete.obs","na.or.complete", or "pairwise.complete.obs".

nbins

A non-negative integer of the number of bins to generate (cutoffs will be generated by the
discretize function from the infotheo package).

bin.cutoffs

A list of values demarcating the bin cutoffs. The binning is
performed using the findInterval function.